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Timing won't alter enough to affect anything unless key is shorn off. If the points have gap--any gap within reason--then it should spark & run. Am wondering if it's the type of flywheel with the built in advance cam & something has come adrift with that--something to check!!.
I did notice that when I took the flywheel off that there was a little arm that actuated a round collar that was frozen up. I cleaned it all up and put a little oil on it so that it would move easier. The little arm was very wobbly and didnt seat right even though the c clip was on correctly. I'm guessing that is the advance cam you were talking about. Maybe I can shim the little arm so it's not as wobbly and see what that does.
Yes that's the advancer & they do wear out in moving parts--the arm pivot & where it locates into the cam. Just grease it up so it moves as nice as you can get & the spring on the arm should have slight tension when right back on retard but not so much tension that it'll struggle to reach full advance. If all else fails you could weld it on advance & forget about it. Anyhow, that's irrelevant to the no spark issue at this stage. Hope you find the lack of spark cause soon. Can be damn frustrating.
Is your bike fitted with either a good quallity condensor or a genuine Yamaha one?
Even though it's new ,there's nowt to say it's not breaking down or in fact the connections good.
If it runs after you replace the flywheel some connection could be getting moved just enough to make contact.
How annoying for you.